Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in .

Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, and yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide a more reliable assessment of susceptibility than traditional methods, we predicted resistance from WGS for 976 bloodstream infection isolates from Oxfordshire, United Kingdom, comparing against phenotypes from the BD Phoenix (calibrated against EUCAST guidelines). A total of 339/976 (35%) isolates were amoxicillin-clavulanate resistant.

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study.

Background: Patients born outside the UK have contributed to a 20% rise in the UK's tuberculosis incidence since 2000, but their effect on domestic transmission is not known. Here we use whole-genome sequencing to investigate the epidemiology of tuberculosis transmission in an unselected population over 6 years.

Methods: We identified all residents with Oxfordshire postcodes with a Mycobacterium tuberculosis culture or a clinical diagnosis of tuberculosis between Jan 1, 2007, and Dec 31, 2012, using local databases and checking against the national Enhanced Tuberculosis Surveillance database.

Congenital toxoplasmosis: continued parasite proliferation in the fetal brain despite maternal immunological control in other tissues.

Background: Congenital toxoplasmosis is a serious condition but little is known of the natural history of parasite development and associated fetal tissue destruction.

Methods: Two cases identified by ultrasound underwent induced abortion at 21 and 30 weeks' gestation. At autopsy, the placenta and fetal organs were examined by histology and immunocytochemistry employing anti-Toxoplasma stage-specific antibodies to confirm diagnosis and also provide information on the stage of parasite development.

Multilocus sequence typing of Clostridium difficile.

A robust high-throughput multilocus sequence typing (MLST) scheme for Clostridium difficile was developed and validated using a diverse collection of 50 reference isolates representing 45 different PCR ribotypes and 102 isolates from recent clinical samples. A total of 49 PCR ribotypes were represented overall. All isolates were typed by MLST and yielded 40 sequence types (STs).

Development of novel treatments for hepatitis C.

Hepatitis C virus (HCV) infection is a major and growing global health problem, affecting about 170 million people worldwide, and is a leading cause of liver cirrhosis and hepatocellular carcinoma. Currently, treatment is restricted to interferon alfa and ribavirin, which leads to a successful outcome in only about 50% of individuals. New effective treatments with tolerable side-effect profiles are needed urgently, but development has been hindered by an inability to culture HCV and a scarcity of animal models.

Urine cytology screening for polyoma virus infection following renal transplantation: the Oxford experience.

Objective: To review the first year of a monthly urine cytology screening service, introduced to identify renal transplant patients at risk of polyoma virus nephropathy (PVN), at an early, potentially treatable, stage.

Methods And Results: Monthly urine samples (n = 392) were received from 97/108 transplant recipients in 2005. Of 56 patients with follow-up >6 months, 20% and 9% had significant (>10 decoy cells/cytospin) and non-significant positive cytology, respectively.

Polygenic control of human T lymphotropic virus type I (HTLV-I) provirus load and the risk of HTLV-I-associated myelopathy/tropical spastic paraparesis.

Human T lymphotropic virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is one outcome of infection with HTLV-I. A population association study of 229 patients with HAM/TSP and 202 healthy carriers of HTLV-I in southern Japan showed that this outcome of HTLV-I infection and the HTLV-I provirus load are under polygenic control. Of 58 polymorphic sites studied in 39 non-HLA candidate gene loci, 3 new host genetic factors that influenced the risk of HAM/TSP or the provirus load of HTLV-I were identified.